Frequently Asked Questions


To import pathways from WikiPathways, follow these steps:

  • Go to Tools > Import pathways from WikiPathways
  • Select the organism for which you wish to download the pathways
  • The drop-down list consists of the organisms for which pathways are available for download from the WikiPathways portal (

If you have downloaded pathways from WikiPathways in the GPML format outside GeneSpring, then you can import these pathways by following these steps:

  • Go to Tools > Import pathways from file > GPML
  • Browse for the pathway files and select WikiPathways as Provider
  • Select the associated organism using Set Organism

All imported pathways are stored in a central pathway database that can be searched via Search > Pathways.

To import pathways from BioCyc ( in GeneSpring, follow these steps:

  • Go to Tools > Import Pathways from BioCyc > From Agilent Server.
  • Select the desired organisms in the Automatic Software Update dialog that opens. Click Update.
  • An Information dialog informs you of the size requirements for downloading all the pathways for the selected organisms. Click OK.
  • Another Information dialog confirms when the download is complete. Click OK.

If you are not able to import pathways from the Agilent Server (for example because of an internet connectivity issue), you can request GeneSpring support to email you an update file for the organisms of your choice and select Tools > Import Pathways from BioCyc > From Update File... instead. You have to save this file to your computer and point to it in the Please Select A .update File dialog. The remaining steps are the same as described above.
All imported pathways are stored in a central pathway database that can be searched via Search > Pathways.

GeneSpring supports the import of pathways from the WikiPathways portal (directly in GeneSpring or as GPML files that were previously downloaded from the portal, also see Q1. How can I import pathways from WikiPathways in GeneSpring?). You can also import pathways from BioCyc directly in GeneSpring (see Q2. How can I import pathways from BioCyc in GeneSpring?). In addition, you can import pathway files in the BioPAX (Level 2 and Level 3, *.owl) , GPML (*.gpml), and Text (*.txt) format.

Every time you update an Interaction Database in GeneSpring, the Update Pathways dialog opens automatically. This dialog allows you to choose which of the pathways that you previously imported into GeneSpring (non-GPML format only) you would like to update or delete based on the new information recorded in the updated Interaction Database. For each pathway the Update Pathways dialog displays updated entities and obsolete entities. If you want to update pathways at a later date, you can return to the Update Pathways dialog through Annotations > Update Pathways.

Yes, deleting a pathway in the Update Pathway dialog will delete the pathway from any experiment it is saved in, as it is permanently deleted from the GeneSpring database.

When importing pathways in the GPML format, GeneSpring identifies duplicate pathways based on pathway name, organism and pathway provider. If duplicate pathways are found, the Resolve Duplicates dialog gives you the choice to

  • rename any of the pathways identified as duplicate and import them,
  • overwrite the existing pathway with the new pathway,
  • ignore duplicate pathways and not import them at all.


Only GPML and BioPax Level 3 pathways can be imported into GeneSpring without the organism’s Interaction Database. However, to import and work with any other file format, the common as well as the organism specific Interaction Databases are required.